Background

Aroma is an important grain quality trait in rice, controlled by mutations within the BADH2 gene. The trait is simply inherited, and its importance in variety development makes it a practical target for marker-assisted selection in applied breeding programs. The predominant functional mutation within BADH2, an 8-bp indel, can be reliably detected using a PCR-based assay, but the available assays and associated genotyping platforms are insufficient for large-scale applied molecular breeding applications and are not compatible with outsourcing genotyping services.

Results

We first characterized SNP diversity across the BADH2 gene in a collection of 2932 rice varieties to determine the number of gene haplotypes in O. sativa. Using 297 gene-based SNPs, 11 haplotype groups were detected, and subsequently identified a minimal set of nine informative SNPs that uniquely identified the BADH2 haplotypes. These nine SNPs were developed into KASP assays and used to examine a panel of 369 U.S. rice accessions. The panel represented modern breeding germplasm and included all known aroma pedigree sources in U.S. rice. Six haplotypes were detected within the U.S. panel, of which two were found in majority (85%) of varieties. A representative set of 39 varieties from all haplotype groups was evaluated phenotypically to distinguish aromatic from non-aromatic lines.

Conclusion

One haplotype (Hap 6) was found to be perfectly associated with the aromatic phenotype. A single KASP SNP unique to Hap 6 was demonstrated to reliably differentiate aromatic from non-aromatic rice varieties across U.S. germplasm.

中文翻译：

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BADH2芳香基因中单倍​​型多样性的表征和预测美国水稻香气的KASP SNP分析方法的发展。

背景

香气是水稻中重要的谷物品质性状，受BADH2基因内的突变控制。该性状是简单遗传的，它在品种开发中的重要性使其成为应用育种计划中标记辅助选择的实际目标。可以使用基于PCR的检测方法可靠地检测到BADH2中主要的功能突变，即8 bp indel，但可用的检测方法和相关的基因分型平台不足以用于大规模应用的分子育种应用，并且与外包基因分型服务不兼容。

结果

我们首先确定了2932个水稻品种中BADH2基因的SNP多样性，从而确定了O. sativa的基因单倍型。使用基于297个基因的SNP，检测到11个单倍型组，随后鉴定出最少的9个能唯一识别BADH2的信息性SNP组。单倍型。这9个SNP被开发为KASP分析方法，并用于检查369种美国大米种质。该小组代表了现代育种种质，包括美国大米中所有已知的香谱系来源。在美国专家组中检测到六种单倍型，其中大多数（85％）品种中发现了两种。表型评价了来自所有单倍型组的39个代表性品种，以区分芳香族和非芳香族。

结论

发现一种单倍型（Hap 6）与芳香表型完美相关。证明了Hap 6特有的单个KASP SNP能可靠地区分美国种质中的芳香族和非芳香族水稻品种。